/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.schemes;\r
\r
+import java.awt.*;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class ColourSchemeProperty\r
{\r
+ /** DOCUMENT ME!! */\r
public static final int CLUSTAL = 0;\r
+\r
+ /** DOCUMENT ME!! */\r
public static final int BLOSUM = 1;\r
+\r
+ /** DOCUMENT ME!! */\r
public static final int PID = 2;\r
+\r
+ /** DOCUMENT ME!! */\r
public static final int ZAPPO = 3;\r
- public static final int HYDROPHOBIC=4;\r
- public static final int HELIX=5;\r
- public static final int STRAND=6;\r
- public static final int TURN = 7;\r
- public static final int BURIED = 8;\r
- public static final int NUCLEOTIDE = 9;\r
- public static final int USER_DEFINED = 10;\r
- public static final int NONE = 11;\r
\r
+ /** DOCUMENT ME!! */\r
+ public static final int TAYLOR = 4;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int HYDROPHOBIC = 5;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int HELIX = 6;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int STRAND = 7;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int TURN = 8;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int BURIED = 9;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int NUCLEOTIDE = 10;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int USER_DEFINED = 11;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int NONE = 12;\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public static int getColourIndexFromName(String name)\r
{\r
- int ret=11;\r
- if(name.equalsIgnoreCase("Clustal"))\r
+ int ret = 12;\r
+\r
+ if (name.equalsIgnoreCase("Clustal"))\r
+ {\r
ret = CLUSTAL;\r
- else if(name.equalsIgnoreCase("Blosum62"))\r
+ }\r
+ else if (name.equalsIgnoreCase("Blosum62"))\r
+ {\r
ret = BLOSUM;\r
- else if(name.equalsIgnoreCase("% Identity"))\r
+ }\r
+ else if (name.equalsIgnoreCase("% Identity"))\r
+ {\r
ret = PID;\r
- else if(name.equalsIgnoreCase("Zappo"))\r
+ }\r
+ else if (name.equalsIgnoreCase("Zappo"))\r
+ {\r
ret = ZAPPO;\r
- else if(name.equalsIgnoreCase("Hydrophobic"))\r
+ }\r
+ else if (name.equalsIgnoreCase("Taylor"))\r
+ {\r
+ ret = TAYLOR;\r
+ }\r
+ else if (name.equalsIgnoreCase("Hydrophobic"))\r
+ {\r
ret = HYDROPHOBIC;\r
- else if(name.equalsIgnoreCase("Helix Propensity"))\r
+ }\r
+ else if (name.equalsIgnoreCase("Helix Propensity"))\r
+ {\r
ret = HELIX;\r
- else if(name.equalsIgnoreCase("Strand Propensity"))\r
+ }\r
+ else if (name.equalsIgnoreCase("Strand Propensity"))\r
+ {\r
ret = STRAND;\r
- else if(name.equalsIgnoreCase("Turn Propensity"))\r
+ }\r
+ else if (name.equalsIgnoreCase("Turn Propensity"))\r
+ {\r
ret = TURN;\r
- else if(name.equalsIgnoreCase("Buried Index"))\r
+ }\r
+ else if (name.equalsIgnoreCase("Buried Index"))\r
+ {\r
ret = BURIED;\r
- else if(name.equalsIgnoreCase("Nucleotide"))\r
+ }\r
+ else if (name.equalsIgnoreCase("Nucleotide"))\r
+ {\r
ret = NUCLEOTIDE;\r
- else if(name.equalsIgnoreCase("User Defined"))\r
- ret = USER_DEFINED;\r
+ }\r
+ else if (name.equalsIgnoreCase("User Defined"))\r
+ {\r
+ ret = USER_DEFINED;\r
+ }\r
\r
return ret;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param cs DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public static String getColourName(ColourSchemeI cs)\r
{\r
- if(cs instanceof ConservationColourScheme)\r
- cs = ((ConservationColourScheme)cs).cs;\r
\r
+ int index = 12;\r
\r
- int index = 11;\r
- if(cs instanceof ClustalxColourScheme)\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
index = CLUSTAL;\r
- else if(cs instanceof Blosum62ColourScheme)\r
+ }\r
+ else if (cs instanceof Blosum62ColourScheme)\r
+ {\r
index = BLOSUM;\r
- else if(cs instanceof PIDColourScheme)\r
+ }\r
+ else if (cs instanceof PIDColourScheme)\r
+ {\r
index = PID;\r
- else if(cs instanceof ZappoColourScheme)\r
+ }\r
+ else if (cs instanceof ZappoColourScheme)\r
+ {\r
index = ZAPPO;\r
- else if(cs instanceof HydrophobicColourScheme)\r
+ }\r
+ else if (cs instanceof TaylorColourScheme)\r
+ {\r
+ index = TAYLOR;\r
+ }\r
+ else if (cs instanceof HydrophobicColourScheme)\r
+ {\r
index = HYDROPHOBIC;\r
- else if(cs instanceof HelixColourScheme)\r
+ }\r
+ else if (cs instanceof HelixColourScheme)\r
+ {\r
index = HELIX;\r
- else if(cs instanceof StrandColourScheme)\r
+ }\r
+ else if (cs instanceof StrandColourScheme)\r
+ {\r
index = STRAND;\r
- else if(cs instanceof TurnColourScheme)\r
+ }\r
+ else if (cs instanceof TurnColourScheme)\r
+ {\r
index = TURN;\r
- else if(cs instanceof BuriedColourScheme)\r
+ }\r
+ else if (cs instanceof BuriedColourScheme)\r
+ {\r
index = BURIED;\r
- else if(cs instanceof NucleotideColourScheme)\r
+ }\r
+ else if (cs instanceof NucleotideColourScheme)\r
+ {\r
index = NUCLEOTIDE;\r
- else if(cs instanceof UserColourScheme)\r
+ }\r
+ else if (cs instanceof UserColourScheme)\r
+ {\r
index = USER_DEFINED;\r
+ }\r
\r
return getColourName(index);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param index DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public static String getColourName(int index)\r
{\r
- String ret=null;\r
- switch(index)\r
- {\r
- case CLUSTAL: ret = "Clustal"; break;\r
- case BLOSUM: ret = "Blosum62"; break;\r
- case PID: ret = "% Identity"; break;\r
- case ZAPPO: ret = "Zappo"; break;\r
- case HYDROPHOBIC: ret="Hydrophobic";break;\r
- case HELIX: ret="Helix Propensity";break;\r
- case STRAND: ret="Strand Propensity";break;\r
- case TURN: ret="Turn Propensity";break;\r
- case BURIED: ret="Buried Index";break;\r
- case NUCLEOTIDE:ret="Nucleotide"; break;\r
- case USER_DEFINED:ret="User Defined";break;\r
- default: ret = "None"; break;\r
+ String ret = null;\r
+\r
+ switch (index)\r
+ {\r
+ case CLUSTAL:\r
+ ret = "Clustal";\r
+\r
+ break;\r
+\r
+ case BLOSUM:\r
+ ret = "Blosum62";\r
+\r
+ break;\r
+\r
+ case PID:\r
+ ret = "% Identity";\r
+\r
+ break;\r
+\r
+ case ZAPPO:\r
+ ret = "Zappo";\r
+\r
+ break;\r
+\r
+ case TAYLOR:\r
+ ret = "Taylor";\r
+ break;\r
+\r
+ case HYDROPHOBIC:\r
+ ret = "Hydrophobic";\r
+\r
+ break;\r
+\r
+ case HELIX:\r
+ ret = "Helix Propensity";\r
+\r
+ break;\r
+\r
+ case STRAND:\r
+ ret = "Strand Propensity";\r
+\r
+ break;\r
+\r
+ case TURN:\r
+ ret = "Turn Propensity";\r
+\r
+ break;\r
+\r
+ case BURIED:\r
+ ret = "Buried Index";\r
+\r
+ break;\r
+\r
+ case NUCLEOTIDE:\r
+ ret = "Nucleotide";\r
+\r
+ break;\r
+\r
+ case USER_DEFINED:\r
+ ret = "User Defined";\r
+\r
+ break;\r
+\r
+ default:\r
+ ret = "None";\r
+\r
+ break;\r
}\r
+\r
return ret;\r
}\r
\r
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param al DOCUMENT ME!\r
+ * @param name DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,\r
+ String name)\r
{\r
- return getColour(al, getColourIndexFromName(name));\r
+ return getColour(al.getSequences(), al.getWidth(), name);\r
}\r
\r
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param seqs DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param name DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static ColourSchemeI getColour(java.util.Vector seqs, int width,\r
+ String name)\r
+ {\r
+ return getColour(seqs, width, getColourIndexFromName(name));\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param seqs DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param index DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static ColourSchemeI getColour(java.util.Vector seqs, int width,\r
+ int index)\r
{\r
ColourSchemeI cs = null;\r
- switch(index)\r
+\r
+ switch (index)\r
{\r
- case CLUSTAL: cs = new ClustalxColourScheme(al.getSequences(), al.getWidth()); break;\r
- case BLOSUM: cs = new Blosum62ColourScheme(); break;\r
- case PID: cs = new PIDColourScheme(); break;\r
- case ZAPPO: cs = new ZappoColourScheme(); break;\r
- case HYDROPHOBIC: cs = new HydrophobicColourScheme(); break;\r
- case HELIX: cs = new HelixColourScheme(); break;\r
- case STRAND: cs = new StrandColourScheme(); break;\r
- case TURN: cs = new TurnColourScheme(); break;\r
- case BURIED: cs = new BuriedColourScheme(); break;\r
- case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;\r
- case USER_DEFINED: cs = new UserColourScheme(null);\r
+ case CLUSTAL:\r
+ cs = new ClustalxColourScheme(seqs, width);\r
+\r
+ break;\r
+\r
+ case BLOSUM:\r
+ cs = new Blosum62ColourScheme();\r
+\r
+ break;\r
+\r
+ case PID:\r
+ cs = new PIDColourScheme();\r
+\r
+ break;\r
+\r
+ case ZAPPO:\r
+ cs = new ZappoColourScheme();\r
+\r
+ break;\r
+\r
+ case TAYLOR:\r
+ cs = new TaylorColourScheme();\r
+ break;\r
+\r
+ case HYDROPHOBIC:\r
+ cs = new HydrophobicColourScheme();\r
+\r
+ break;\r
+\r
+ case HELIX:\r
+ cs = new HelixColourScheme();\r
+\r
+ break;\r
+\r
+ case STRAND:\r
+ cs = new StrandColourScheme();\r
+\r
break;\r
\r
- default: break;\r
+ case TURN:\r
+ cs = new TurnColourScheme();\r
+\r
+ break;\r
+\r
+ case BURIED:\r
+ cs = new BuriedColourScheme();\r
+\r
+ break;\r
+\r
+ case NUCLEOTIDE:\r
+ cs = new NucleotideColourScheme();\r
+\r
+ break;\r
+\r
+ case USER_DEFINED:\r
+ Color[] col = new Color[24];\r
+ for (int i = 0; i < 24; i++)\r
+ {\r
+ col[i] = Color.white;\r
+ }\r
+ cs = new UserColourScheme(col);\r
+ break;\r
+\r
+ default:\r
+ break;\r
}\r
\r
return cs;\r
}\r
+\r
+ public static Color getAWTColorFromName(String name)\r
+ {\r
+ Color col = null;\r
+ name = name.toLowerCase();\r
+ if (name.equals("black"))\r
+ {\r
+ col = Color.black;\r
+ }\r
+ else if (name.equals("blue"))\r
+ {\r
+ col = Color.blue;\r
+ }\r
+ else if (name.equals("cyan"))\r
+ {\r
+ col = Color.cyan;\r
+ }\r
+ else if (name.equals("darkGray"))\r
+ {\r
+ col = Color.darkGray;\r
+ }\r
+ else if (name.equals("gray"))\r
+ {\r
+ col = Color.gray;\r
+ }\r
+ else if (name.equals("green"))\r
+ {\r
+ col = Color.green;\r
+ }\r
+ else if (name.equals("lightGray"))\r
+ {\r
+ col = Color.lightGray;\r
+ }\r
+ else if (name.equals("magenta"))\r
+ {\r
+ col = Color.magenta;\r
+ }\r
+ else if (name.equals("orange"))\r
+ {\r
+ col = Color.orange;\r
+ }\r
+ else if (name.equals("pink"))\r
+ {\r
+ col = Color.pink;\r
+ }\r
+ else if (name.equals("red"))\r
+ {\r
+ col = Color.red;\r
+ }\r
+ else if (name.equals("white"))\r
+ {\r
+ col = Color.white;\r
+ }\r
+ else if (name.equals("yellow"))\r
+ {\r
+ col = Color.yellow;\r
+ }\r
+\r
+ return col;\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff